Data Model

Hierarchy

Data in a Flywheel system is organized in a tree-like hierarchy, as indicated in the following diagram.

../../../static/images/data-model.png
  • User - An authorized entity, usually referenced by email address.
  • Group - A grouping of users and projects.
  • Project - A project represents a grouping of subjects and sessions, e.g. within a study.
  • Subject - An individual under study.
  • Session - A grouping of acquired data, typically data acquired within a limited timeframe.
  • Acquisition - A set of one or more files, typically acquired as part of the same process, at the same time.
  • AnalysisOutput - A set of one or more derivative files from analyzing files after they have been acquired.

Permissions

Permissions in Flywheel are managed at the Group and Project level. Users that belong to a Group or a Project have a Role, which is one of:

  • Admin (admin) - Administrators can perform administrative-level actions such as setting permissions or creating and deleting projects.
  • Read-Write (rw) - Users can read, create and delete data, but cannot assign permissions or delete entire projects.
  • Read-Only (ro) - Users can only read data

By default when a new Project is created belonging to a Group, permissions will be copied from the Group to the Project, keeping user roles intact. From that point on, permissions for that Project must be managed at that project, changes made to the Group will not propagate to the project.

# See project permissions
project = fw.get(projectId);
disp(project.permissions{1});

# Add permission to a project
project.addPermission(flywheel.model.Permission('id', 'justinehlert@flywheel.io', 'access', 'ro'));

# Remove permission from a project
project.deletePermission(projectId, 'justinehlert@flywheel.io');

Containers

Projects, Subjects, Sessions, Acquisitions and Analyses are all different types of Containers. Containers in Flywheel all support the following features:

Tags

Tags are concise labels that provide descriptive metadata that can be searched on. Available tags are managed on the Group.

# See tags on a session
session = fw.get(sessionId);
fprintf('%s\n', strjoin(session.tags, ', '));

# Add a tag to a session
session.addTag('Control');

# Remove a tag from a session
session.deleteTag('Analysis Required');

Notes

Notes are user-entered, human readable metadata attached to a container. They are timestamped and attributed to the user that entered them.

# See notes on a session
session = fw.get(sessionId);
disp(session.notes{1});

# Add a note to a session
session.addNote('This is a note');

# Delete a note from a session
session.deleteNote(session.notes{1}.id);

Info

Info is free-form JSON metadata associated with a container or file.

# Print the info for an acquisition
acquisition = fw.get(acquisitionId);
disp(acquisition.info);

# Replace the entire contents of acquisition info
acquisition.replaceInfo(struct('splines', 34));

# Add additional fields to acquisition info
acquisition.updateInfo(struct('curve', 'bezier'));

# Delete fields from acquisition info
acquisition.deleteInfo({{'splines'; 'bezier'}});

Files

Files are a set of file attachments associated with a container. See also Dealing with Files.

# List files on an acquisition
acquisition = fw.get(acquisitionId);

for idx = 1:numel(acquisition.files)
  fprintf('Name: %s, type: %s\n', acquisition.files{idx}.name, acquisition.files{idx}.type);
end

# Upload a file to an acquisition
acquisition.uploadFile('/path/to/file.txt');

# Download a file to disk
acquisition.downloadFile('file.txt', '/path/to/file.txt');

# Files can also have metadata
disp(acquisition.files{1}.info);

acquisition.replaceFileInfo('file.txt', struct('wordCount', 327));

File Classification

Flywheel supports an extensible, multi-dimenstional classification scheme for files. Each dimension of classification is referred to as an aspect. The available aspects are determined by the file’s modality.

For example, the MR modality provides the Intent, Measurement and Features aspects. In addition, the Custom aspect is always available, regardless of modality.

% Display the aspects defined in the MR modality
mr = fw.get_modality('MR');
keys = mr.classification.keys();
for i = 1:numel(keys)
        aspectName = keys{i};
        aspectValues = strjoin(mr.classification.(aspectName), ', ');
        fprintf('%s: %s\n', aspectName, aspectValues);
end

% Replace a file's modality and classification
acquisition.replaceFileClassification('file.txt', ...
        struct('Intent', {{'Structural'}}, 'Measurement', {{'T2'}}),
        'modality', 'MR');

% Update a file's Custom classification, without changing
% existing values or modality
acquisition.updateFileClassification('file.txt', ...
        struct('Custom', {{'value1', 'value2'}}));

% Delete 'value1' from Custom classification
acquisition.deleteFileClassification('file.txt', ...
        struct('Custom', {{'value1'}}));

Timestamps [NEW]

Objects with timestamps and created/modified dates provide helper accessors to get those dates in the local (system) timezone, as well as the original timezone in the case of acquisition and session timestamps.

For example:

% Acquisition Timestamp (tz=UTC)
disp(acquisition.timestamp);

% Acquisition Timestamp (tz=Local Timezone)
disp(acquisition.localTimestamp);

% Acquisition Timestamp (tz=Original Timezone)
disp(acquisition.originalTimestamp);

Age at Time of Session [NEW]

Sessions have a field for subject age at the time of the session, in seconds. There are also helper accessors to get age in years, months, weeks and days.

For example:

% Subject age in seconds
fprintf('Subject was %0.2f seconds old\n', session.age);

% Subject age in years
fprintf('Subject was %0.2f years old\n', session.ageYears);